Systems and methods for inferring cell status

Abstract

Systems and methods for inferring a status of a cell population are provided. Described techniques allow deconvolving a first clonal population comprising a first plurality of cells of a species, wherein nucleic acid sequence reads from each cell in the first plurality of cells are obtained. The nucleic acid sequence reads are mapped into bins representing portions of a reference genome, and a pattern of sequence read counts for each cell across the multiple bins is used to assign a cell to a group, thereby inferring a mitotic status of the cell. The assignment of nucleic acid sequence reads into bins is also be used for segregating cells into classes based on a status of a certain biological marker in each cell. Comparison of sequence read counts for a subset of bins across the cell classes allows evaluating effect of a compound on a cell status.

1 - 43 . (canceled) 
     
     
         44 . A method of deconvolving a heterogeneous population of cells comprising a first plurality of cells, the method comprising:
 at a computer system having one or more processors, and memory storing one or more programs for execution by the one or more processors:   (A) obtaining a set of nucleic acid sequence reads from each cell in the first plurality of cells through a single cell sequencing process, thereby obtaining a first plurality of sets of nucleic acid sequence reads, wherein each respective set of nucleic acid sequence reads in the first plurality of sets of nucleic acid sequence reads is from a single cell in the first plurality of cells;   (B) mapping a nucleic acid sequence of each respective sequence read in each respective set of sequence reads onto a corresponding bin in a plurality of bins, wherein each respective bin in the plurality of bins represents a different portion of a reference genome of the species, thereby obtaining a nucleic acid sequence read count for each respective bin in the plurality of bins for each respective cell in the first plurality of cells;   (C) independently segregating each respective cell in the first plurality of cells into one of a plurality of cell classes based on a presence, absence, or amount of a marker or a marker set in the respective cell;   (D) for each respective cell in each respective cell class in the plurality of cell classes, assigning the respective cell into one of a plurality of groups based upon a pattern of sequence read counts of the respective cell across the plurality of bins, wherein   a first group in the plurality of groups represents a first mitotic stage,   a second group in the plurality of groups represents a non-mitotic stage, and   the assigning (D) determines whether the respective cell is to be assigned to the first group by applying a first mitotic filter to the nucleic acid read count of respective bins in the plurality of bins obtained for the respective cell; and   (E) comparing a proportion of cells in each cell class in the plurality of cell classes that are in the first mitotic stage.   
     
     
         45 . The method of  claim 44  wherein the single cell sequencing process is a single cell DNA sequencing process and each nucleic acid sequence read in each set in the first plurality of sets of nucleic acid sequence reads is a DNA sequence. 
     
     
         46 . The method of  claim 44  wherein the single cell sequencing process is a single cell RNA sequencing process and each nucleic acid sequence read in each set in the first plurality of sets of nucleic acid sequence reads is an RNA sequence. 
     
     
         47 . The method of  claim 44  wherein the marker or the marker set comprises a predetermined genetic mutation and the segregating (C) determines whether the respective cell includes the predetermined genetic mutation, wherein, when the respective cell includes the predetermined genetic mutation the respective cell is deemed to belong to a first class in the plurality of cell classes and when the respective cell does not include the predetermined genetic mutation, the respective cell is deemed to belong in a class in the plurality of cell classes other than the first class. 
     
     
         48 . The method of  claim 47  wherein the predetermined genetic mutation is a single nucleotide polymorphism, an insertion, a deletion, or an inversion. 
     
     
         49 . The method of  claim 44  wherein the marker or marker set is a plurality of predetermined genetic mutations and the segregating (C) determines whether the respective cell includes each predetermined genetic mutation in the plurality of predetermined genetic mutations, wherein, when the respective cell includes each predetermined genetic mutation in the plurality of predetermined genetic mutations, the respective cell is deemed to belong to a first class in the plurality of cell classes and when the respective cell does not include each predetermined genetic mutation in the plurality of predetermined genetic mutations the respective cell is deemed to belong in a class in the plurality of cell classes other than the first class. 
     
     
         50 . The method of  claim 49  wherein each predetermined genetic mutation in the plurality of predetermined genetic mutations is a single nucleotide polymorphism, an insertion, a deletion, or an inversion. 
     
     
         51 . The method of  claim 49  wherein the marker is a threshold number of genetic mutations mapping to one or more predetermined portions of the reference genome and the segregating (C) determines whether the respective cell includes the threshold number of genetic mutations, wherein, when the respective cell includes the threshold number of genetic mutations, the respective cell is deemed to belong to a first class in the plurality of cell classes and when the respective cell does not include the threshold number of genetic mutations, the respective cell is deemed to belong in a class in the plurality of cell classes other than the first class. 
     
     
         52 . The method of  claim 51  wherein the threshold number is determined by evaluating an average number and standard deviation of the average number of mutations in the one or more predetermined portions of the reference genome across the first plurality of cells. 
     
     
         53 . The method of  claim 51  wherein each genetic mutation mapping to the one or more predetermined portions of the reference genome is a single nucleotide polymorphism, an insertion, a deletion, or an inversion in the one or more predetermined portions of the reference genome. 
     
     
         54 . The method of  claim 51  wherein each genetic mutation mapping to the one or more predetermined portions of the reference genome is a single nucleotide polymorphism, an insertion, a deletion, or an inversion in the one or more predetermined portions of the reference genome. 
     
     
         55 . The method of  claim 51  wherein the one or more predetermined portions of the reference genome consists of the X-Ray Repair Cross Complementing 2 (XRCC2) gene, the X-Ray Repair Cross Complementing 3 (XRCC3) gene, the RAD54 gene, the H2AX gene, the phosphatase and tensin homolog gene, and/or the ATM gene. 
     
     
         56 . The method of  claim 44  wherein
 the species is human, 
 each bin in the plurality of bins is the same size and the plurality of bins collectively encompass at least three percent of the entire human genome, and 
 the plurality of bins consists of between one hundred and two thousand bins. 
 
     
     
         57 . The method of  claim 44 , the method further comprising:
 (F) obtaining a set of nucleic acid sequence reads from each cell in a second plurality of cells of the species through a single cell sequencing process, thereby obtaining a second plurality of sets of nucleic acid sequence reads, wherein each respective set of nucleic acid sequence reads in the second plurality of sets of nucleic acid sequence reads is from a single cell in the second plurality of cells and the second plurality of cells has been exposed to a compound;   (G) mapping a nucleic acid sequence of each respective sequence read in each respective set of sequence reads in the second plurality of sets of nucleic acid sequence reads onto a corresponding bin in the plurality of bins;   (H) for each respective cell in the second plurality of cells, independently segregating the respective cell into one of the plurality of cell classes based on the presence, absence, or amount of the marker or the marker set in the respective cell;   (I) for each respective cell in each respective cell class in the plurality of cell classes for the second plurality of cells, assigning the respective cell into one of the plurality of groups based upon a pattern of sequence read counts of the respective cell across the plurality of bins by applying the first mitotic filter to the nucleic acid read count of respective bins in the plurality of bins obtained for the respective cell; and   (J) comparing a proportion of cells in each cell class in the plurality of cell classes that are in the first mitotic stage between the first plurality of cells and the second plurality of cells.   
     
     
         58 . The method of  claim 57 , wherein the second plurality of cells is exposed to the compound for at least one hour prior to performing the obtaining (F). 
     
     
         59 . The method of  claim 57 , wherein the compound is DNA repair inhibitor. 
     
     
         60 . The method of  claim 57 , wherein the compound is an organic compound having a molecular weight of less than 2000 Daltons. 
     
     
         61 . The method of  claim 57 , wherein the compound is an organic compound that satisfies the Lipinski rule of five criteria. 
     
     
         62 . The method of  claim 57 , wherein the compound is an organic compound that satisfies at least three criteria of the Lipinski rule of five criteria. 
     
     
         63 . The method of  claim 57 , wherein the compound is a poly ADP ribose polymerase (PARP) inhibitor. 
     
     
         64 . The method of  claim 44 , wherein the first plurality of cells is heterogeneous. 
     
     
         65 . The method of  claim 44 , wherein the first plurality of cells is from a tumor biopsy. 
     
     
         66 . A computer system having one or more processors, and memory storing one or more programs for execution by the one or more processors, the one or more programs comprising instructions for performing the method of  claim 44 . 
     
     
         67 . A non-transitory computer readable storage medium, wherein the non-transitory computer readable storage medium stores instructions, which when executed by a computer system, cause the computer system to perform the method of  claim 44 . 
     
     
         68 .- 131 . (canceled)